Here's an interesting little mod I thought up whilst at work today. Unfortunately I can't test it at the moment since I am at work, but it should work ok...
Essentially what I've done is change the ability of the spy character. No longer can it spy (which I found useless and boring anyway). This means no more pain in the ass unrest, no more pointless spying missions and no more spy opening gates, which incidentally was a nice feature but ultimately one that the AI never could use to its advantage. Spy missions were too easy (always 95-100%), as was getting experience with them, and this lead to an AI obsession for building Thieves Guilds everywhere.
Instead, what the spy can do now is build forts (mainly for watchtower) and sabotage, something the AI never/rarely used its assassins for anyway (I'm still not sure how this will work in terms of seeing the buildings within the settlements given there's no spy now...). Anyway, the build forts was chosen as I always hated having to run my named characters to the borders of regions to build forts. Named characters can still do this, but this role is also given to the spy.
The traits have been adjusted to keep with the 'spying' tradition, but they're triggered now by sabotage missions instead. Spies still gain bonuses to the line of sight so they can still function as spies.
Let me know if you like it or indeed whether there are any errors (or if it doesn't work!). It may also need some fine tuning.